comparison bwa-0.6.2/simple_dp.c @ 0:dd1186b11b3b draft

Uploaded BWA
author ashvark
date Fri, 18 Jul 2014 07:55:14 -0400
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-1:000000000000 0:dd1186b11b3b
1 #include <stdlib.h>
2 #include <stdio.h>
3 #include <unistd.h>
4 #include <string.h>
5 #include <zlib.h>
6 #include <stdint.h>
7 #include "stdaln.h"
8 #include "utils.h"
9
10 #include "kseq.h"
11 KSEQ_INIT(gzFile, gzread)
12
13 typedef struct {
14 int l;
15 unsigned char *s;
16 char *n;
17 } seq1_t;
18
19 typedef struct {
20 int n_seqs, m_seqs;
21 seq1_t *seqs;
22 } seqs_t;
23
24 unsigned char aln_rev_table[256] = {
25 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
26 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
27 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
28 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
29 'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
30 'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
31 'N','t','v','g', 'h','N','N','c', 'd','N','N','m', 'N','k','N','N',
32 'N','N','y','s', 'a','N','b','w', 'x','r','N','N', 'N','N','N','N',
33 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
34 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
35 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
36 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
37 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
38 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
39 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
40 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
41 };
42
43 static int g_is_global = 0, g_thres = 1, g_strand = 0, g_aa = 0;
44 static AlnParam g_aln_param;
45
46 static void revseq(int len, uint8_t *seq)
47 {
48 int i;
49 for (i = 0; i < len>>1; ++i) {
50 uint8_t tmp = aln_rev_table[seq[len-1-i]];
51 seq[len-1-i] = aln_rev_table[seq[i]];
52 seq[i] = tmp;
53 }
54 if (len&1) seq[i] = aln_rev_table[seq[i]];
55 }
56
57 static seqs_t *load_seqs(const char *fn)
58 {
59 seqs_t *s;
60 seq1_t *p;
61 gzFile fp;
62 int l;
63 kseq_t *seq;
64
65 fp = xzopen(fn, "r");
66 seq = kseq_init(fp);
67 s = (seqs_t*)calloc(1, sizeof(seqs_t));
68 s->m_seqs = 256;
69 s->seqs = (seq1_t*)calloc(s->m_seqs, sizeof(seq1_t));
70 while ((l = kseq_read(seq)) >= 0) {
71 if (s->n_seqs == s->m_seqs) {
72 s->m_seqs <<= 1;
73 s->seqs = (seq1_t*)realloc(s->seqs, s->m_seqs * sizeof(seq1_t));
74 }
75 p = s->seqs + (s->n_seqs++);
76 p->l = seq->seq.l;
77 p->s = (unsigned char*)malloc(p->l + 1);
78 memcpy(p->s, seq->seq.s, p->l);
79 p->s[p->l] = 0;
80 p->n = strdup((const char*)seq->name.s);
81 }
82 kseq_destroy(seq);
83 gzclose(fp);
84 fprintf(stderr, "[load_seqs] %d sequences are loaded.\n", s->n_seqs);
85 return s;
86 }
87
88 static void aln_1seq(const seqs_t *ss, const char *name, int l, const char *s, char strand)
89 {
90 int i;
91 for (i = 0; i < ss->n_seqs; ++i) {
92 AlnAln *aa;
93 seq1_t *p = ss->seqs + i;
94 g_aln_param.band_width = l + p->l;
95 aa = aln_stdaln_aux(s, (const char*)p->s, &g_aln_param, g_is_global, g_thres, l, p->l);
96 if (aa->score >= g_thres || g_is_global) {
97 printf(">%s\t%d\t%d\t%s\t%c\t%d\t%d\t%d\t%d\t", p->n, aa->start1? aa->start1 : 1, aa->end1, name, strand,
98 aa->start2? aa->start2 : 1, aa->end2, aa->score, aa->subo);
99 // NB: I put the short sequence as the first sequence in SW, an insertion to
100 // the reference becomes a deletion from the short sequence. Therefore, I use
101 // "MDI" here rather than "MID", and print ->out2 first rather than ->out1.
102 for (i = 0; i != aa->n_cigar; ++i)
103 printf("%d%c", aa->cigar32[i]>>4, "MDI"[aa->cigar32[i]&0xf]);
104 printf("\n%s\n%s\n%s\n", aa->out2, aa->outm, aa->out1);
105 }
106 aln_free_AlnAln(aa);
107 }
108 }
109
110 static void aln_seqs(const seqs_t *ss, const char *fn)
111 {
112 gzFile fp;
113 kseq_t *seq;
114 int l;
115
116 fp = xzopen(fn, "r");
117 seq = kseq_init(fp);
118 while ((l = kseq_read(seq)) >= 0) {
119 if (g_strand&1) aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '+');
120 if (g_strand&2) {
121 revseq(l, (uint8_t*)seq->seq.s);
122 aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '-');
123 }
124 }
125 kseq_destroy(seq);
126 gzclose(fp);
127 }
128
129 int bwa_stdsw(int argc, char *argv[])
130 {
131 int c;
132 seqs_t *ss;
133
134 while ((c = getopt(argc, argv, "gT:frp")) >= 0) {
135 switch (c) {
136 case 'g': g_is_global = 1; break;
137 case 'T': g_thres = atoi(optarg); break;
138 case 'f': g_strand |= 1; break;
139 case 'r': g_strand |= 2; break;
140 case 'p': g_aa = 1; break;
141 }
142 }
143 if (g_strand == 0) g_strand = 3;
144 if (g_aa) g_strand = 1;
145 if (optind + 1 >= argc) {
146 fprintf(stderr, "\nUsage: bwa stdsw [options] <seq1.long.fa> <seq2.short.fa>\n\n");
147 fprintf(stderr, "Options: -T INT minimum score [%d]\n", g_thres);
148 fprintf(stderr, " -p protein alignment (suppressing -r)\n");
149 fprintf(stderr, " -f forward strand only\n");
150 fprintf(stderr, " -r reverse strand only\n");
151 fprintf(stderr, " -g global alignment\n\n");
152 fprintf(stderr, "Note: This program is specifically designed for alignment between multiple short\n");
153 fprintf(stderr, " sequences and ONE long sequence. It outputs the suboptimal score on the long\n");
154 fprintf(stderr, " sequence.\n\n");
155 return 1;
156 }
157 g_aln_param = g_aa? aln_param_aa2aa : aln_param_blast;
158 g_aln_param.gap_end = 0;
159 ss = load_seqs(argv[optind]);
160 aln_seqs(ss, argv[optind+1]);
161 return 0;
162 }